Shinji and Nyota
by gunman
Summary: After Spocks departure from Starfleet, Nyota Uhura latches onto Shinji Ikari for emotional support, which becomes something much more intimate for the pair. Lemon. Takes place during 'Star Trek Beyond'.


_**SHINJI AND NYOTA  
**_by Gunman

Disclaimer: I do not own Evangelion or Star Trek Beyond, or their characters.

Summary: This is an alternate on Star Trek and Evangelion, with Shinji being a genetically enhanced being like Khan and getting together with Uhura.

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(Stardate 2263.2)

Captain James T. Kirk has returned from the Teenaxi Delegation meeting, and somewhat failed to broker a treaty with them on behalf of the Fibonan Republic. The Teenaxians immense paranoia of the Fibonans wanting to eat them lead to their 'assault' on Captain Kirk, and forcing him to teleport back to _The Enterprise_.

Scotty had just beamed Kirk up to the ship, along with two uninvited Teenaxi guests, who were small, lizard-like creatures, and apparently quite vicious.

"Get him off! Get Him Off!" the first security officer shouted.

"Over here!" the second officer shouted.

"Watch Out!"

"I ripped my shirt again." Kirk groaned as he stepped out of the Transporter Room.

"How'd it go?" Scotty asked, just as a Teenaxian slammed into the glass wall in front of the console he was sitting at.

Walking through the corridors of the ship, his boot in one hand, the strange weapon piece in the other, he was greeted and soon accompanied by two members of his senior staff.

"Captain, were your efforts to broker a treaty between the Teenaxian and Fibonan Republic successful?" Commander Shinji Ikari asked him.

"Uh... let's just say I came up short. Could you... put that in the vault, Shinji, please? Thanks." Kirk said to Shinji as he tossed the artifact to the genetically-enhanced young man.

"Jim, you look like crap." Dr. Leonard 'Bones' McCoy said as Shinji turned down the other corridor towards the Archive Vault.

"Thank you, Bones." Kirk groaned as he continued to limp down the corridor to his room.

"You got that little vein popping out of your temple again. You okay?" McCoy asked.

"Never better! Just another day in the fleet." Kirk laughed as he continued down the corridor.

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"Captain's Log, Stardate 2263.2. Today is our 966th day in deep space, a little under three years into our five-year mission. The more time we spend out here, the harder it is to tell where one day ends and the next one begins. It can be a challenge to feel grounded when even gravity is artificial. But, well, we do what we can to make it feel like home. The crew, as always, continues to act admirably despite the rigors of our extended stay here in outer space. And the personal sacrifices they have made. We continue to search for new life forms in order to establish firm diplomatic ties. Our extended time in uncharted territory has stretched the ship's mechanical capacities. But fortunately our engineering department, led by Mr. Scott, is more than up to the job. Mr. Ikari continues to prove a valuable science officer, as well as a hard working replacement to Mr. Spock, who had long left us to continue his work on New Vulcan. The new crew members, including Dr. Carol Marcus and Lieutenant T'Pol, have also shown amazing talent and adaptiveness, as well as teamwork savvy. The ship aside, prolonged cohabitation has definitely had effects on interpersonal dynamics. Some experiences for the better, and some for the worse. As for me, things have started to feel a little episodic. The farther out we go, the more I find myself wondering what it is we're trying to accomplish. If the universe is truly endless, then are we not striving for something forever out of reach? _The Enterprise _is scheduled for a reprovisioning stop at _Yorktown_, the Federation's newest and most advanced starbase. Perhaps a break from routine will offer up some respite, from the mysteries of the unknown."

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Lieutenant Nyota Uhura was conflicted, if anything.

Prior to the start of the _Enterprises_ five-year mission to deep space, Spock had resigned his commission in Starfleet in order to participate in the new Vulcan breeding program to save his species from extinction.

Since the destruction of their home world by the rogue Romulan named Nero, the Vulcan race had been diminished to less than 10,000. Ambassador Spock, from the future, had inadvertently provided a means to cause his own planets destruction. As such, he had devised a way to help save his species.

During the reconstruction and upgrading of the _Enterprise_, after their battle against the genetically augmented tyrant named Khan, Ambassador Spock had taken ill. Spock was contacted by his father, Sarek, about this, and asked Spock to return to help with the rebuilding of their race.

Deeming it logical and important, Spock had left to be involved in the new breeding program, along with another member of the crew, Rei Ayanami.

Prior to the conflict on Kronos, and the bombing of the London Archive, the blue-haired albino and her half-brother, Shinji Ikari, had come from another dimension and phased through the genetically augmented terrorist who called himself Khan, then known as John Harrison, both gaining his abilities and intellect.

However, Khan's genetic enhancements, combined with their own unique genetics, caused a very unusual transformation in the pair. They were physically aged from 14 to 21 years of age. They were able to hide this fact from Starfleet and smuggled themselves on-board the _Enterprise _in order to stop both Khan and Starfleet from making a tremendous mistake.

While they were enroute to Kronos, the pair, along with Dr. Carol Wallace, revealed their true natures to Captain Kirk and the crew.

After the battle against the Klingons on Kronos, Khan is brought aboard the _Enterprise_ where they are all interrogated and medically treated, even though they didn't need it.

Spock and Rei hit it off immediately, seeing as how they were more alike than anyone else on the ship. Shinji provided as much information as he could, his newly enhanced genetic form giving him access to more knowledge, and emotions, than ever before.

When Admiral Marcus and his new ship, the _USS Vengeance_, arrived, Kirk was forced to escape and head back to Earth. Marcus caught up with him and bombed The _Enterprise_, killing several crew members and damaging the ship. They were saved by Montgomery Scott, who had managed to sneak aboard the _Vengeance_ prior to it's departure to Kronos and sabotage it, allowing Kirk and Khan to space-jump towards the warship and sneak aboard, in order to take the ship from within.

Kirk would have taken Shinji and Rei with him, but they were too inexperienced to be of much help. And Spock was needed on the _Enterprise_ to captain it.

However, once they had taken the ship, Kirk had Scotty stun Khan since he didn't trust him. As a result, Khan ended their alliance and took out Scotty, Carol Marcus and Kirk, before killing Admiral Marcus with his bare hands, and then ordered the other 72 cryogenically imprisoned Augments, Khans crew, to be beamed over to him from the _Enterprise_.

However, Spock, along with Dr. McCoy, Shinji, Rei, and every technician, science and medical officer aboard _the Enterprise_, had removed the augments from the long-range torpedo tubes, and triggered them to detonate once Khan began to fire on their ship.

_The Enterprise_ was damaged and without power, forcing Shinji to go into the radioactive reactor chamber of the warp core and realign the housings that provided the ship energy. The radiation would have killed a normal person, but Shinji's newly gained regenerative abilities managed to save him.

It took less than a week for Shinji to fully recover.

Through Spock's and Kirk's efforts, Khan was recaptured and put back into cryo-stasis along with the rest of his crew, and Shinji and Rei were made members of the _Enterprise_ crew by Kirk as a 'thank you' for everything they had done.

During the year-long reconstruction of the _Enterprise_, Spock tested Shinji and Rei and found their intellect to be surpassing all available Starfleet technicians and science officers. With the exception of himself and Khan.

However, two months prior to _the Enterprises_ departure from Earth for their five-year mission, Spock received a message that Ambassador Spock had taken ill and might not make it. Spock decided to resign his commission in Starfleet and travel to New Vulcan in order to continue 'his' work.

Rei decided to go with him.

Spock named Shinji as his replacement, feeling confident that the human-Augment was up to the task, both intellectually and morally, of First Officer and Archivist aboard the _Enterprise_.

Uhura, upset by this, did not speak to Spock before he left. Mostly because he left with Rei.

While she had nothing against either Rei or Shinji, she was upset that Spock had chosen to accept the blue-haired albino rather quickly, despite their years together.

It was now almost three years into their five-year mission and _The_ _Enterprise_ was on it's way to _The_ _Yorktown_, the newest and most advanced space station in the Federation. Uhura hoped that she could at least find a nice little place to drown her sorrows and emotions that she had been keeping bottled up while on their three years away from Earth

Since Spock's departure, Uhura had turned to Shinji as a shoulder to lean on and an ear to listen. Shinji had no problem with this. Perhaps he filled a void in her life that Spock had, both as a science officer, a friend and someone who was physically more than she was. Shinji actually felt the same.

Not that she specifically needed the last one, but it was nice to have someone care for her who was also capable of protecting her from any other possible threat.

Shinji, she found, was nice, quiet, kind, hard-working, helpful and considerate of others. She had been shocked to find out that before his arrival in this world, he was a major introvert and had more than a few confidence issues. His phasing through Khan had given him more of a backbone than he had before, but he was still a decent sort. Khans aggressive nature conflicted with Shinji's original meekness apparently it made him more balanced. This made him no less of a gentleman, who didn't try and take advantage of the emotionally hurt communications officer.

But unlike some of the other crew members of _The Enterprise_, Nyota had yet to consummate any kind of relationship with anyone. This included Shinji, with whom she was closer to than most.

A years worth of reconstruction for _the Enterprise_, and nearly three years in space, Shinji was now 25 years old, and Uhura was now 29 years old.

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Kirk and McCoy were in the Officers private lounge, having a small celebration to Kirk's upcoming birthday, when they received a call from the Bridge.

"Kirk here." the Captain said.

"Captain, approaching _Yorktown_ base." Hikaru Sulu said.

"I'm on my way, Mr. Sulu."

The pair stepped onto the Bridge, where Shinji and the others were waiting for them.

"Wow. That is impressive." Chekov said as he took in the gigantic circular space station which was covered in a see-through glass-like dome.

"Aye. She's a beauty, isn't she?" Scotty remarked.

"What a damn monstrosity! Couldn't we just rent some space on a planet?" McCoy snarked.

"Showing geographical favoritism among inducted Federation worlds has the potential to cause diplomatic tension amongst our allies." Shinji stated, stating the obvious facts in the case, as well as doing a very good impression of the departed Mr. Spock.

"You don't think that looks tense? Looks like a damn snow globe in space just waiting to break!" McCoy snapped.

"That's the spirit, Bones." Kirk said in exasperation.

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Once _the Enterprise _was docked at _the Yorktown_, the senior officers approving the resupplying of their various medical, technical and provisional supplies, Nyota goes to one of the local bars to get drunk.

Shinji finds her later and helps her back to his apartment, since he doesn't know where she is residing, where she sleeps off her hangover

She woke up a few hours later.

"I feel terrible." Uhura groaned.

"Six Pints of Romulan Ale, with nothing to eat, you should be dead." Shinji said as he set a tray of food down next to her.

She looked under the covers she felt around her body, finding her uniform still on and her underwear still intact, and no moisture around herself.

_He didn't take advantage of me._ She thought to herself. She was also a little confused that she hadn't wet herself, having drunk six pints of Romulan Ale in one sitting.

However, that thought triggered the undesired response.

"Where's the bathroom?" she asked.

"Through there." he said, pointing behind her.

"Be right back." she said as she hustled herself into the room.

Five minutes later, she returned.

"Tea?" he asked.

"Uh, thank you." she said, accepting the drink.

"Is something wrong?" he asked.

"Umm... well, you didn't..."

"Take advantage of you?"

She shrugged her shoulders as she gave him a weak smile.

"I respect you too much to do that, Uhura." he said.

"You can call me Nyota, if you want, Shinji."

"You know, considering all the things you can do, both intellectually and physically, I'm a little surprised that you don't have a girlfriend already. Like T'Pol."

Shinji said nothing in regards to the female Vulcan medical officer that Spock had approved of just prior to his departure from Starfleet. McCoy was a little put off by her sometimes blunt, emotionless demeanor, but her professionalism and medical knowledge was second-to-none.

T'Pol, named after her late Grandmother, was a brilliant and gifted medical student and scientist. She was also the only other person aboard the _Enterprise_ who could match Shinji in terms of intellect and physicality.

"Being First Officer of the Enterprise, not to mention the Archivist and Science officer, has taken up a lot of my time. Including learning all the protocols and rules and proper procedures of Starfleet itself. Which also includes the moral aspects of being an Officer."

Nyota gave him a dirty look.

"Is something wrong?" he asked.

"Sorry, you... just sound like Spock." she said.

"I didn't mean to. I was only stating the truth."

'_Sigh_.' "I know. I didn't mean to snap. It's just that I'm still pretty sore that he up and left like he did. And with your sister no less."

"Half-sister." he corrected.

"Whatever. I'm still upset about that." she said.

"Why? It's been almost three years since they left." he said.

"Yeah. To be part of the Vulcan breeding program."

"Oh. _That's _why you're upset. That he chose Rei and not you."

"I could have given up my commission. Gone with him."

"He wouldn't have let you."

"I know he's got more in common with her than he did me, but... all those years we were together, I thought they would have meant something to him."

"I'm sorry."

"Don't be. You didn't do anything."

Nyota smiled at him.

"Still a little introverted, aren't you?" she asked.

"A little." he said with a smile.

"Aren't you supposed to be superior to us mere humans?"

"Ha!" he laughed. "I'm only five times stronger and twice as intelligent as a human being can possibly be. Even I can be beaten."

"Nice to see you're humble about it." she said.

"Is something wrong?"

"I... you didn't answer my question."

"About why I am alone?"

"Yes. I mean... I would have thought you and T'Pol..."

"We're friends, but she doesn't consider me a challenge."

"A challenge?" she asked.

"We are... similar... in a lot of ways. I guess she's looking for someone with... differences."

"Oh. But... did you..."

"I thought about it. But... she didn't interest me as... certain others do."

"I see." she said. "What about Gaila?"

"She was seeing someone else at the time."

Deciding to leave the question alone for the moment, Nyota changed subjects.

"Where are we?" she asked.

"My room at the Chrysanthemum Inn." Shinji said.

"Classic Japanese. Old style."

"After being on a star ship for nearly three years, it seemed appropriate."

"It's beautiful here." she said as she looked out at the lavish and intricate Zen garden.

"That's what I thought when I made my reservations." Shinji said. "I was going to have breakfast. Care to join me?"

Uhura smiled.

"Sure." she said.

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The pair had breakfast and spent the day together.

They visited several shops where Nyota got several new dresses which looked sexy on her. Shinji 'was forced' to get a new suit that made him look handsome.

They had lunch and then took in a Holo-Show. There was an afternoon performance of the classical music play called The Samurai and the Princess. Being Japanese, Shinji was interested in seeing it. Nyota went with him.

When dinner rolled around Shinji treated Nyota to something special.

"I never figured you for Italian, Shinji. Nor did I expect you to cook it yourself."

"I did most of the cooking when Rei and I lived alone."

"That's right. You never did tell me just what your life was before you got were teleported here."

"It's a long story."

"Then I'll eat very slow." she said with a smile.

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"That was a wonderful day, Shinji. Thank you." Nyota said as Shinji walked her back to her room at the Chrysanthemum Inn, which was right next to Shinji's.

"You're welcome." Shinji said to her. "I guess I'll see you tomorrow."

"You... don't have to go." she said, tugging on his arm.

"Nyota... are you sure?" he asked, feeling more attracted to her than before.

"I am." she said as she pulled him close. "I don't want to be alone anymore."

"Neither do I."

Their lips met as their bodies pressed tightly against each other. Nyota pulled him into her room, and closed the door.

Shinji's hands caressed Nyota through her dress, finding her zipper and slowly pulling it down. She moaned into his mouth, feeling her dress slowly come undone. She pulled back for second before her hands grabbed his shirt and pulled it up and over his head. She ran her hands over his athletic chest, admiring his nearly perfect-looking muscles.

"Like what you're feeling?" he asked.

"I do." she smiled.

Once she was done with her caressing, she pulled her dress off and let it fall to the floor. Wearing only her white lace bra and panties, Shinji couldn't help but stare at the beautiful communications officer.

"Like what you see?" she asked.

"I do." he asked.

He wrapped his arms around her body, pulling her flush against him, kissing her lips hotly as he held her tightly. His hands caressed her skin, sliding down her back to caress her shapely ass. Nyota was moaning into his mouth, her tongue darting into his to battle with his tongue. This surprised Shinji, but he enjoyed it nonetheless.

"Shinji." she panted almost breathlessly.

"You are so beautiful." he whispered into her ear.

"Show me... all of you." she whispered back, gripping his belt and pants and forcefully pushing them down.

He gripped the hem of her panties and pulled them down her long legs. While he did that, Nyota reached back and unclipped her bra, pulling it from her body.

The now naked pair just stared into each others eyes, their lips brushing lightly against each other, teasingly so.

Shinji picked Nyota up and carried her over to his bed, the pair kissing intimately as they went. When he got to the futon-bed, he set her down and crawled on top of her.

He kissed his way down her body, taking a couple minutes to attend to her perfect breasts. Nyota gasped as she held his head in her hands, enjoying the feeling of her lover suckling her chest. Shinji eventually moved lower, kissing her flat stomach and then coming to the juncture between her legs. She gasped when she felt his tongue invade her already moist womanhood. Her back arched up to the ceiling, her chest sticking up as Shinji expertly delved into her.

She ran her fingers through his hair as he continued to pleasure her, sending her body into extreme convolutions she had never before experienced.

"AAAAAAAAAAHHHHHHHHHHHHH!" she cried out as she came.

Her body was already sweating as Shinji sat up on his knees looking down at the beautiful woman. She stared at him, lust in her eyes as she ran her hands over breasts, as if trying to entice him more than he already was.

She then looked down and saw his fully aroused manhood, and wondered if he had been like that naturally or if it was part of his augmentation.

She threw the thought away as he took her hands and pulled her up and into his lap.

"AH!" She gasped as she suddenly found herself impaled on his large rod.

'_So tight_.' he thought as he held her close, before starting to pump into this galactic beauty.

"Uh, Uh, Uh, Uh, Uh, Uh, Uh, Oh, Oh! Oh, God! Shinji..." Nyota gasped with each forceful thrust of Shinji's manhood into her body.

The black beauty was sitting in the human augments lap, bouncing up and down, her arms and legs wrapped around his body, her head arched back as her eyes were closed shut, just enjoying the feeling of him pounding her.

Shinjis focus was on her bouncing breasts that were rubbing against his chest as he held her firmly, delivering as much pleasure to her as he could. His hands were on her shapely ass, controlling her actions so as to give her as much delight as he could.

Shinji leaned down and licked her right nipple, before latching onto it like a leech and suckling it like a very hungry baby.

Nyota wrapped her arms around his head, her body overheating and on the verge of collapsing. The pleasure was so good, she knew she couldn't last.

"Uh, Uh, SHINJI! SHINJI!" she cried out as the orgasm hit, both lovers coming together in a forceful explosion of passion that nearly overwhelmed them both.

Their bodies were slowly settling down as they held each other close against each other.

"Oh, Shinji. That was..." Nyota panted as she rested her head against his shoulder.

"Yes. You were." Shinji said as he held her tight against him.

She lifted her head up and kissed his lips softly.

"Again." she said to him.

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It was hours later, a few more until it was 'breakfast time'.

Nyota was lying face down on the bed, her breathing deep and shallow, when she felt a pair of hands slide across her wrists and intertwine his fingers with her own.

"Nyota." he whispered into her ear, the black beauty feeling the familiar weight of her lover atop her.

"Uh... Shinji?" she panted as she lifted her head to look back at him. "Again?"

"I can go ALL night." He whispered back to her.

"I think... five times... is my limit." she gasped.

He kissed her shoulder gently as he got off of her and settled in next to her.

"Yes. I think so." he said as he pulled her into a warm hug. "But next time... let's try for six."

Nyota laughed as she rested her head against his chest and let sleep take her away.

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Shinji and Nyota were sleeping peacefully in Nyota's room, the sexy communications officer feeling very satisfied. Nyota awoke first, feeling Shinji was holding her from behind, his naked chest pressed against her back. Nyota could feel his arms wrapped around her, his soft breath blowing through her hair.

Struggling to wake up, shifting in his arms and realizing he was already awake.

"Good morning." he said to her.

"Oh... what time is it?" Nyota asked groggily.

"Noon. A little after." Shinji said.

"We slept most of the day?"

"I wore you out well enough." he replied.

"Yes. You did. Thank you for that."

BEEP-BEEP

"Oh, really?" Nyota grumbled as Shinji got up, crawled over to his pants, and pulling out his communicator.

"Captain?" Shinji asked as he turned it on.

"All key personnel are ordered to return to _The Enterprise_. We have a rescue mission." Kirk said.

Shinji and Nyota looked at each other, sighing in disappointment.

"Well, we signed up for this." he said.

"We did." she sighed.

The pair were quickly dressed and grabbing some energy drinks before heading back to their ship.

The pair stopped before they exited the room. Shinji caressed the side of her face before pressing his lips against hers tenderly.

"I want to do this again." Shinji said to her.

"Oh, we will. Trust me on that." She smiled to her lover.

Shinji kissed her again, but stopped before things got heated once more.

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Authors Notes: 

Here's another lemon crossover story in which I have paired Shinji with Uhora from the new Kelvin Timeline Star Trek movies. Something I have been working on for a while. Hope everyone enjoys it.


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